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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa04LNT0252700.1

CCTTCACCTTCTCCAGCGAGGCACCGGCGCACCGCCTCCACCTCCCTCTCATCCAATCCTTCTGTTCCTCACACCCCTTCCCCTCCCTCTCGCCGGGCAAGTGCCACTACCCTGTCGTCATCCACCTCACTCTTCTCTCCCTTGACCAGGCCAGCGCAAGCTTGTGACGGCCAGATCCGGTGCCCTTGAGCTCGAGACGGACAGATCCGGCGCCCTTGTGCTCGGTGCCACCGGATCCAGCCCCAATGCGACGTAGTGGAGGCGGCAAGAGGGAGAGGGCCGCCAGATCCAGTCAAGACCCGCTATTTTCTTCTCCAGCCGTCGTGGCGGCGGAAGCATGCTCGATCCCCAGCCCCCCAGGACCTGAGGGTGGGGGTTGGGACGCCGTTGCATGTGACACTCGATGAGGAGTGTCCACGCGCCGTGGACGCATTCGACCACCACGCTTCACGGCTGCTTCATACCATGGAGCTCCTCGGTCGCCACAGGAATCATTTACCTCTTATGGTTGGCTTCAAGCTCTACTTCGCTAGCTAAGCTATTTTCCCAATCCCATGGAAAATAAGGAAGCAGAGTACAGCTAAAGGTCCAAGCAGAGGTTTTAACACCATGGCTGGTAGCAAATAGTGGCATGTTATTTTTGAGTGCTACAGTGATCTTACAATGACGGAAATATACCTGGTTCATGGTTAGTATCAATTCCTTTTCTTTTGCTGAACATTCTTTTTCTTTACTCGGTATCAGACTCTTATCTTATCCCCTGTATCATGTGCACTTGCCTAGCCACCTTCACTTTACTACACTGTTTTTGCTGCTAAAAAAACAACCCTTGTAAAGAATGACTCTATCCATGCTTCAGTATTGCGTATATGATTAAATTGACACCCCTATTATATGCATTTAAATGTGTCATGTACTGCAAACAACATAATAATAAAGCATTTAGTTCAACTACTGACCTACTACTACCACATAGTATCTAATTAGTAATACTATGATCTTGGCATGGTCAATTATCCAACTGTGCTGTACAATTAGTAATGTCCTAGTAGTGTTTTTCATCCTCTTGGCGTAGTTATTTAATCAATGTAGCTAATATGAATTTTGTATCAAACCTAGACAATCATGAAGAGAAAATTGCTTTCGACTTCCATAGATTATATCTTGCTCAACTGCTTTGTGAGAATCTACCTAGTTAATACACATCTTCTATGCAATGTACCTAGTATGACTACTCTCCATGTCAGTACTATGTTTTGGTTATGATTTTGCATAATTGCTGATTGAACATTAGCTGATACCTAAATTTTGTTATTTCACTCGTTGACAAATGCTGATTGAGCAATGCTATTCTAACAGTAAGATACATCTCTTTATACAACCTTTTTAGCTCTTCCCGTATCATGTTCAGAACAGAGGTAGTTAGATTAACATTTATGTATAAAATTTCCCTATCAACCGGCTTTTGTTTTTTGAAAATTTGTGGAGCCCTTGTCAAATGATTATTGTATTGTTGAATATAAGGTTATCTTAGTAAATTCATATACCCGAGGCTATGTCCAATTTCTCCCTTATGCATGAATATTGTTGTGCTAGTCTTTGTAAGAATTAGTTTCACTTCACCTACATTTACTTATATGTACCTGAATCATACATAGTAATGAGTCCATTTCTTTTGCTGAGCCTATTTTTTTCTTTAGTATCAAACACCCTTGTAAAGAATGACCAGGTATTCATGCTTCAGCATTGCATACATGATTAAATTGACACCGTTATTTTAGGCATTTAAATGTGTCATATGTACTGCAGATCAGTAATGATCTTTTGGCCAGATCAATTATCCAATTGAGTTGTATCTGAGTCCTGCTAGTGTTTTTCATCCTCTTGGCATAGTTTTTTAATCATCGTAGCTATACATGAATTTTGTAACAAATCTAGGCAATAATGAAGAAATCATGCACAAGTTCAGATTACCTTATTGTTGTCGATTTGCCGAGATCATTTATTTATCTTGTTCAATGGCTTTGTGAGAACCTACCTAAATAATTCTTACCTCTTCTATGCAATCTCAGGGTATCAAAATTAACCGGCTACTGGTAATCATCCGAGGTGCTGTCAAATGACCTACGACGCCATTTGTCAACATTTTTCTAGTTGCATGGCCTCTTGGTTGCCCAAGGATGTACTCATATGTAGGAAGTATTGTTCAGATTCATCTCAGTTGTAGCTGTTCCCGAGATTGGTATTGCTAGTTTTAGATTACATTGTTG

Coding Potentia
Explanation CPC Score
noncoding -1.34087
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0252700.1 4 8764789 T C
Osa04LNT0252700.1 4 8764827 G C
Osa04LNT0252700.1 4 8765013 T C
Osa04LNT0252700.1 4 8767156 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0252700.1 osa-miR5830 Cleavage 4.0 13.957 1 24
Osa04LNT0252700.1 osa-miR156b-3p Translation 5.0 12.484 1 21
Osa04LNT0252700.1 osa-miR171a Cleavage 5.0 16.506 1 21
Osa04LNT0252700.1 osa-miR171b Cleavage 4.0 16.506 1 21
Osa04LNT0252700.1 osa-miR171c-3p Cleavage 4.0 16.506 1 21
Osa04LNT0252700.1 osa-miR171d-3p Cleavage 4.0 16.506 1 21
Osa04LNT0252700.1 osa-miR171e-3p Cleavage 4.0 16.506 1 21
Osa04LNT0252700.1 osa-miR171f-3p Cleavage 4.0 16.506 1 21
Osa04LNT0252700.1 osa-miR1428a-3p Translation 4.5 18.103 1 21
Osa04LNT0252700.1 osa-miR1854-3p Translation 5.0 14.813 1 22
Osa04LNT0252700.1 osa-miR2122 Cleavage 5.0 18.657 1 22
Osa04LNT0252700.1 osa-miR5491 Cleavage 5.0 12.817 1 21
Osa04LNT0252700.1 osa-miR5519 Translation 4.0 11.78 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0252700.1 4 qPEN-4 Morphological trait Panicle/flower RG190 RG908
Osa04LNT0252700.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0252700.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252700.1 4 nan Morphological trait Root RM261 RZ69
Osa04LNT0252700.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
Osa04LNT0252700.1 4 qSNP-4a Morphological trait Panicle/flower RM401 RM335
Osa04LNT0252700.1 4 qCER4-1 Morphological trait Shoot/Seedling RG190 RZ69
Osa04LNT0252700.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0252700.1 4 spp4-2 Morphological trait Panicle/flower RG449 CDO456
Osa04LNT0252700.1 4 gwt4a Morphological trait Seed RG788 RG190
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus